Table 2.

Upstream promotor sequence motifs

Clustera%bMotifcBinding factorMAP scoredPutative functione
145ATGTAYGGRTGRap1p150Ribosomal (G, BF)
111YYNCCNGGCRNNAUnknown 10Ribosomal (G)
2, 425, 26GNGATGAGMTfUnknown 82RNA metabolism (G)
310GCCAATCAGHAP CCAAT-binding complex 23Mitochrondrial (G, BF)
310YTGGGCRGCUnknown 13Mitochrondrial (G)
415TYCGTNNNWNGTGAAbf1p 18RNA metabolism (G)/translation (BF)
516TGTTTCARASte12p 33Mating/cell cycle (G, BF)
137.5GCMCTGCGMKUnknown 11Unknown
1425GGTGGCAARpn4p 73Protein degradation (G, BF)
  • a Cluster numbers are as in Fig. 5.

  • b Percentage of genes in that particular cluster which contain the motif within 600 bp upstream of the transcription start site.

  • c Only motifs with a MAP score greater then 10 and whose motif is confined to a single cluster are included (25). Y is C or T; R is A or G; N is A, C, G, or T; W is A or T; M is A or C; and K is G or T.

  • d MAP score is a statistical value of how “good” a particular motif is and is based on the alignment and the frequency of occurrence in noncoding sequences.

  • e Function of the majority of the genes in the cluster containing the motif (G) or genes known to be controlled by the indicated binding factor (BF).

  • f This consequence sequence has been identified upstream of many RNA polymerase A and C subunit genes and has been referred to as the PAC box (8).